library(knitr)
packageVersion("knitr")
## [1] '1.20'
library(energy)
packageVersion("energy")
## [1] '1.7.5'
library(broom)
packageVersion("broom")
## [1] '0.5.0'
library(plyr)
packageVersion("plyr")
## [1] '1.8.4'
library(kableExtra)
packageVersion("kableExtra")
## [1] '0.9.0'
library(foreach)
packageVersion("foreach")
## [1] '1.4.4'
library(doParallel)
## Loading required package: iterators
## Loading required package: parallel
packageVersion("doParallel")
## [1] '1.0.14'
set.seed(0)
load(file = "diabetes_curated.Rdata")
epsilon=1e-6
nominal_dcor_pvalues <- sapply(1:pathway_number, function(x) (epsilon+(sum(surrogate_dcor[[x]]>dcor_results[x])))/(1+num_simulation))
names(nominal_dcor_pvalues) <- names( pathway_collapsed)
head(sort(nominal_dcor_pvalues),10)
## KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP
## 0.0000000001
## GROSS_HYPOXIA_VIA_HIF1A_UP
## 0.0002000001
## WHITFIELD_CELL_CYCLE_G2
## 0.0002000001
## MA_MYELOID_DIFFERENTIATION_DN
## 0.0003000001
## CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP
## 0.0004000001
## REACTOME_CHROMOSOME_MAINTENANCE
## 0.0005000001
## WIERENGA_STAT5A_TARGETS_UP
## 0.0006000001
## REACTOME_MEIOTIC_SYNAPSIS
## 0.0009000001
## REACTOME_MEIOSIS
## 0.0010000001
## MORI_SMALL_PRE_BII_LYMPHOCYTE_UP
## 0.0010000001
dcor_significant_pathways_p.value <- sort(nominal_dcor_pvalues[nominal_dcor_pvalues <0.05])
length(dcor_significant_pathways_p.value)
## [1] 251
nominal_dcor_q_values <- p.adjust(nominal_dcor_pvalues , method = "fdr")
# nominal_dcor_q_values
nominal_dcor_q_values_under_25 <- sort(nominal_dcor_q_values[nominal_dcor_q_values<0.25])
length((nominal_dcor_q_values_under_25))
## [1] 3
nominal_dcor_q_values_under_25
## KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP
## 0.0000003525
## GROSS_HYPOXIA_VIA_HIF1A_UP
## 0.2350001175
## WHITFIELD_CELL_CYCLE_G2
## 0.2350001175
nrow(gsea_results_significant)
## [1] 170
length(rownames(gsea_results_significant[gsea_results_significant$FDR.q.val<0.25,]))
## [1] 0
Mutually_identified_in_GSEA_dcor <- intersect(names(dcor_significant_pathways_p.value), rownames(gsea_results_significant))
Mutually_identified_in_GSEA_dcor
## [1] "GROSS_HYPOXIA_VIA_HIF1A_UP"
## [2] "REACTOME_CHROMOSOME_MAINTENANCE"
## [3] "REACTOME_MEIOTIC_SYNAPSIS"
## [4] "REACTOME_MEIOSIS"
## [5] "LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_UP"
## [6] "MORI_IMMATURE_B_LYMPHOCYTE_UP"
## [7] "LANDIS_ERBB2_BREAST_TUMORS_65_UP"
## [8] "SMID_BREAST_CANCER_ERBB2_UP"
## [9] "REACTOME_MRNA_CAPPING"
## [10] "FERRANDO_TAL1_NEIGHBORS"
## [11] "REACTOME_TRANSCRIPTION_COUPLED_NER_TC_NER"
## [12] "REACTOME_NUCLEOTIDE_EXCISION_REPAIR"
## [13] "OHGUCHI_LIVER_HNF4A_TARGETS_UP"
## [14] "GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_UP"
## [15] "PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP"
## [16] "WONG_MITOCHONDRIA_GENE_MODULE"
## [17] "SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER"
## [18] "FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN"
## [19] "KEGG_OXIDATIVE_PHOSPHORYLATION"
## [20] "KEGG_HUNTINGTONS_DISEASE"
## [21] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13"
## [22] "REACTOME_DNA_REPAIR"
## [23] "MOOTHA_VOXPHOS"
Mutually_identified_in_GSEA_dcor_fdr <- intersect(names(nominal_dcor_q_values_under_25),rownames(gsea_results_significant[gsea_results_significant$FDR.q.val<0.25,]))
length(Mutually_identified_in_GSEA_dcor_fdr)
## [1] 0
Significant_in_dcor_not_in_GSEA <- setdiff(names(dcor_significant_pathways_p.value),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(dcor_significant_pathways_p.value[Significant_in_dcor_not_in_GSEA],gsea_results[Significant_in_dcor_not_in_GSEA,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities%>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP | WHITFIELD_CELL_CYCLE_G2 | MA_MYELOID_DIFFERENTIATION_DN | CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP | WIERENGA_STAT5A_TARGETS_UP | MORI_SMALL_PRE_BII_LYMPHOCYTE_UP | SHEPARD_CRUSH_AND_BURN_MUTANT_UP | HEIDENBLAD_AMPLICON_12P11_12_UP | WANG_TARGETS_OF_MLL_CBP_FUSION_DN | FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP | ZHANG_TLX_TARGETS_60HR_DN | BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN | SMITH_TERT_TARGETS_DN | GEORGES_TARGETS_OF_MIR192_AND_MIR215 | ZHENG_FOXP3_TARGETS_IN_THYMUS_UP | FRIDMAN_IMMORTALIZATION_DN | LEE_DIFFERENTIATING_T_LYMPHOCYTE | MITSIADES_RESPONSE_TO_APLIDIN_UP | FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS | FOSTER_TOLERANT_MACROPHAGE_UP | ENK_UV_RESPONSE_KERATINOCYTE_DN | IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP | DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER | WALLACE_PROSTATE_CANCER_RACE_UP | PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7 | WIERENGA_STAT5A_TARGETS_GROUP1 | ENGELMANN_CANCER_PROGENITORS_DN | HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN | OUILLETTE_CLL_13Q14_DELETION_DN | FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN | WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP | CAFFAREL_RESPONSE_TO_THC_DN | PID_EPHA_FWDPATHWAY | BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP | SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP | BHAT_ESR1_TARGETS_VIA_AKT1_UP | OISHI_CHOLANGIOMA_STEM_CELL_LIKE_DN | LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP | PID_PTP1B_PATHWAY | BIOCARTA_PAR1_PATHWAY | GARY_CD5_TARGETS_DN | BIOCARTA_CARDIACEGF_PATHWAY | QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2 | JAEGER_METASTASIS_DN | REACTOME_PI3K_AKT_ACTIVATION | BROWNE_HCMV_INFECTION_48HR_UP | WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN | REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX | REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA | BORCZUK_MALIGNANT_MESOTHELIOMA_UP | REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING | LIU_PROSTATE_CANCER_UP | FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL | GEISS_RESPONSE_TO_DSRNA_DN | HORTON_SREBF_TARGETS | KEGG_RNA_POLYMERASE | REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5 | PID_PRL_SIGNALING_EVENTS_PATHWAY | FORTSCHEGGER_PHF8_TARGETS_UP | HOUSTIS_ROS | ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN | KEGG_STEROID_BIOSYNTHESIS | SANSOM_APC_TARGETS_DN | LABBE_WNT3A_TARGETS_DN | BOCHKIS_FOXA2_TARGETS | REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING | CHEBOTAEV_GR_TARGETS_DN | VERHAAK_GLIOBLASTOMA_NEURAL | MACLACHLAN_BRCA1_TARGETS_UP | PID_EPHA2_FWD_PATHWAY | DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN | REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT | REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE | BIOCARTA_CDC42RAC_PATHWAY | NAGASHIMA_NRG1_SIGNALING_DN | TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP | PLASARI_TGFB1_TARGETS_10HR_DN | REACTOME_REGULATORY_RNA_PATHWAYS | PID_S1P_S1P3_PATHWAY | DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP | PID_TGFBR_PATHWAY | PLASARI_NFIC_TARGETS_BASAL_UP | SHI_SPARC_TARGETS_UP | PID_S1P_S1P1_PATHWAY | KEGG_PYRIMIDINE_METABOLISM | MULLIGHAN_NPM1_SIGNATURE_3_UP | PID_LIS1_PATHWAY | PID_S1P_S1P2_PATHWAY | REACTOME_MICRORNA_MIRNA_BIOGENESIS | HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS | BROWNE_HCMV_INFECTION_6HR_DN | PID_AVB3_INTEGRIN_PATHWAY | PID_ECADHERIN_KERATINOCYTE_PATHWAY | PETRETTO_CARDIAC_HYPERTROPHY | CHEN_ETV5_TARGETS_TESTIS | SHEN_SMARCA2_TARGETS_UP | REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING | BROWNE_HCMV_INFECTION_4HR_DN | PID_WNT_NONCANONICAL_PATHWAY | DAZARD_RESPONSE_TO_UV_NHEK_DN | RIGGI_EWING_SARCOMA_PROGENITOR_DN | PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP | BIOCARTA_RAS_PATHWAY | MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN | LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q | GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN | ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP | ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN | SA_TRKA_RECEPTOR | REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE | PID_SYNDECAN_4_PATHWAY | PETROVA_PROX1_TARGETS_UP | GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN | GAJATE_RESPONSE_TO_TRABECTEDIN_UP | REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION | RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP | BERNARD_PPAPDC1B_TARGETS_UP | NUYTTEN_NIPP1_TARGETS_UP | KASLER_HDAC7_TARGETS_1_DN | MENSE_HYPOXIA_UP | KENNY_CTNNB1_TARGETS_DN | ONDER_CDH1_TARGETS_1_UP | BASAKI_YBX1_TARGETS_UP | WINZEN_DEGRADED_VIA_KHSRP | RODWELL_AGING_KIDNEY_NO_BLOOD_DN | MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP | PID_P53_REGULATION_PATHWAY | WIERENGA_STAT5A_TARGETS_GROUP2 | UEDA_PERIFERAL_CLOCK | WANG_SMARCE1_TARGETS_UP | PID_ECADHERIN_NASCENT_AJ_PATHWAY | BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP | SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY | WINNEPENNINCKX_MELANOMA_METASTASIS_DN | REACTOME_G_ALPHA1213_SIGNALLING_EVENTS | LEIN_CHOROID_PLEXUS_MARKERS | TARTE_PLASMA_CELL_VS_PLASMABLAST_DN | LIN_NPAS4_TARGETS_UP | NADLER_HYPERGLYCEMIA_AT_OBESITY | SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP | JOHNSTONE_PARVB_TARGETS_3_UP | RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP | COATES_MACROPHAGE_M1_VS_M2_DN | MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP | PENG_RAPAMYCIN_RESPONSE_UP | BILD_MYC_ONCOGENIC_SIGNATURE | MCCLUNG_COCAINE_REWARD_5D | HU_ANGIOGENESIS_DN | LENAOUR_DENDRITIC_CELL_MATURATION_DN | ODONNELL_METASTASIS_DN | CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP | PETRETTO_HEART_MASS_QTL_CIS_DN | MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP | CADWELL_ATG16L1_TARGETS_DN | VANTVEER_BREAST_CANCER_ESR1_UP | MASSARWEH_RESPONSE_TO_ESTRADIOL | DE_YY1_TARGETS_UP | GUILLAUMOND_KLF10_TARGETS_DN | BIOCARTA_EDG1_PATHWAY | ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP | SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1 | REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER | MARKS_HDAC_TARGETS_UP | NOJIMA_SFRP2_TARGETS_UP | BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN | HASLINGER_B_CLL_WITH_MUTATED_VH_GENES | BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS | LIU_SOX4_TARGETS_UP | BIOCARTA_RACCYCD_PATHWAY | FARMER_BREAST_CANCER_APOCRINE_VS_BASAL | SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN | FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP | PUJANA_BRCA2_PCC_NETWORK | SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP | MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5 | REACTOME_MRNA_SPLICING_MINOR_PATHWAY | REACTOME_RNA_POL_III_TRANSCRIPTION | COATES_MACROPHAGE_M1_VS_M2_UP | AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN | REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER | AMIT_EGF_RESPONSE_40_MCF10A | GOLUB_ALL_VS_AML_DN | MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN | CUI_GLUCOSE_DEPRIVATION | MOREIRA_RESPONSE_TO_TSA_UP | GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP | RICKMAN_METASTASIS_UP | BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN | MANALO_HYPOXIA_DN | BIOCARTA_P53HYPOXIA_PATHWAY | YAMASHITA_METHYLATED_IN_PROSTATE_CANCER | GUTIERREZ_MULTIPLE_MYELOMA_UP | BIOCARTA_PTDINS_PATHWAY | VERRECCHIA_EARLY_RESPONSE_TO_TGFB1 | TIAN_TNF_SIGNALING_NOT_VIA_NFKB | VARELA_ZMPSTE24_TARGETS_UP | LI_INDUCED_T_TO_NATURAL_KILLER_DN | MURAKAMI_UV_RESPONSE_6HR_DN | PID_AVB3_OPN_PATHWAY | REACTOME_PEROXISOMAL_LIPID_METABOLISM | SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN | SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP | MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED | BRUECKNER_TARGETS_OF_MIRLET7A3_UP | ENGELMANN_CANCER_PROGENITORS_UP | YAGI_AML_WITH_T_8_21_TRANSLOCATION | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1 | GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP | PID_VEGFR1_2_PATHWAY | LAMB_CCND1_TARGETS | LEE_TARGETS_OF_PTCH1_AND_SUFU_DN | MURAKAMI_UV_RESPONSE_24HR | GENTILE_UV_LOW_DOSE_UP | KEGG_COLORECTAL_CANCER | KEEN_RESPONSE_TO_ROSIGLITAZONE_UP | ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP | PID_IL4_2PATHWAY | JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP | MISSIAGLIA_REGULATED_BY_METHYLATION_UP | REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING | RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN | KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT | YAGI_AML_RELAPSE_PROGNOSIS | BURTON_ADIPOGENESIS_6 | REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT | MIKKELSEN_ES_ICP_WITH_H3K4ME3 | REACTOME_CHOLESTEROL_BIOSYNTHESIS | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.0000 | 0.0002 | 0.0003 | 0.0004 | 0.0006 | 0.0010 | 0.0010 | 0.0011 | 0.0011 | 0.0014 | 0.0014 | 0.0017 | 0.0019 | 0.0020 | 0.0021 | 0.0025 | 0.0028 | 0.0030 | 0.0032 | 0.0033 | 0.0034 | 0.0035 | 0.0036 | 0.0039 | 0.004 | 0.0046 | 0.0049 | 0.0051 | 0.0058 | 0.0059 | 0.0061 | 0.0061 | 0.0062 | 0.0064 | 0.0066 | 0.0073 | 0.0079 | 0.0080 | 0.0081 | 0.0085 | 0.0090 | 0.0093 | 0.0094 | 0.0098 | 0.010 | 0.0101 | 0.0102 | 0.0104 | 0.0108 | 0.0110 | 0.0116 | 0.0118 | 0.0118 | 0.0118 | 0.0118 | 0.0120 | 0.0124 | 0.0124 | 0.0127 | 0.0127 | 0.0134 | 0.0138 | 0.0141 | 0.0147 | 0.0147 | 0.0149 | 0.0150 | 0.0153 | 0.0153 | 0.0158 | 0.0162 | 0.0162 | 0.0164 | 0.0169 | 0.0171 | 0.0171 | 0.0173 | 0.0174 | 0.0176 | 0.0178 | 0.0178 | 0.0179 | 0.0180 | 0.0183 | 0.0184 | 0.0186 | 0.0187 | 0.0189 | 0.0192 | 0.0193 | 0.0197 | 0.0198 | 0.020 | 0.0201 | 0.0201 | 0.0203 | 0.0206 | 0.0208 | 0.0208 | 0.0210 | 0.0211 | 0.0211 | 0.0213 | 0.0219 | 0.0220 | 0.0223 | 0.0224 | 0.0224 | 0.0225 | 0.0228 | 0.0231 | 0.0236 | 0.0241 | 0.0245 | 0.0247 | 0.0251 | 0.0251 | 0.0251 | 0.0253 | 0.0253 | 0.0255 | 0.0259 | 0.0261 | 0.0262 | 0.0262 | 0.0264 | 0.0266 | 0.0267 | 0.0270 | 0.0271 | 0.0275 | 0.0277 | 0.0280 | 0.0283 | 0.0283 | 0.0284 | 0.0285 | 0.0288 | 0.0289 | 0.0290 | 0.0291 | 0.0294 | 0.0299 | 0.0300 | 0.0303 | 0.0303 | 0.0305 | 0.0306 | 0.0323 | 0.0323 | 0.0331 | 0.0334 | 0.0335 | 0.0339 | 0.0339 | 0.0339 | 0.0340 | 0.0346 | 0.0346 | 0.0347 | 0.0347 | 0.0348 | 0.0353 | 0.0354 | 0.0355 | 0.0355 | 0.0356 | 0.036 | 0.0361 | 0.0362 | 0.0363 | 0.0367 | 0.0370 | 0.0371 | 0.0372 | 0.0372 | 0.0375 | 0.0377 | 0.0379 | 0.0379 | 0.0382 | 0.0384 | 0.0386 | 0.0389 | 0.0389 | 0.0395 | 0.0399 | 0.0399 | 0.0400 | 0.0401 | 0.0410 | 0.0410 | 0.0412 | 0.0415 | 0.0416 | 0.0418 | 0.0422 | 0.0422 | 0.0429 | 0.0432 | 0.0433 | 0.0436 | 0.0436 | 0.0441 | 0.0442 | 0.0445 | 0.0445 | 0.0447 | 0.0448 | 0.0452 | 0.0452 | 0.0453 | 0.0454 | 0.0457 | 0.0460 | 0.0469 | 0.0471 | 0.0472 | 0.0474 | 0.048 | 0.0481 | 0.0483 | 0.0485 | 0.0485 | 0.0488 | 0.0491 | 0.0491 | 0.0499 |
| GSEA | 0.7939 | 0.9876 | 0.2189 | 0.2354 | 0.2618 | 0.5202 | 0.1169 | 0.5246 | 0.7294 | 0.1394 | 0.1515 | 0.6320 | 0.3854 | 0.2096 | 0.8133 | 0.7462 | 0.7427 | 0.0977 | 0.6335 | 0.3752 | 0.6447 | 0.9084 | 0.4907 | 0.7976 | 0.497 | 0.2470 | 0.7563 | 0.5545 | 0.1467 | 0.7864 | 0.2458 | 0.7019 | 0.3020 | 0.8959 | 0.2016 | 0.7410 | 0.5279 | 0.2785 | 0.9792 | 0.2609 | 0.3593 | 0.4626 | 0.6437 | 0.8517 | 0.917 | 0.4706 | 0.1566 | 0.0541 | 0.2172 | 0.8423 | 0.1959 | 0.1481 | 0.7030 | 0.0813 | 0.6083 | 0.3138 | 0.1454 | 0.3533 | 0.2560 | 0.6378 | 0.2281 | 0.6826 | 0.1972 | 0.8822 | 0.4839 | 0.2924 | 0.0671 | 0.2548 | 0.3777 | 0.5885 | 0.2110 | 0.7505 | 0.3730 | 0.6747 | 0.7375 | 0.1127 | 0.1750 | 0.9283 | 0.4038 | 0.9014 | 0.8059 | 0.7820 | 0.4008 | 0.9248 | 0.3119 | 0.3037 | 0.3267 | 0.3840 | 0.2688 | 0.4038 | 0.9648 | 0.0855 | 0.996 | 0.3123 | 0.8800 | 0.5264 | 0.8546 | 0.9123 | 0.6963 | 0.4346 | 0.5838 | 1.0000 | 0.7234 | 0.9403 | 0.2385 | 0.0638 | 0.4255 | 0.2464 | 0.4812 | 0.8540 | 0.6598 | 0.5322 | 0.7256 | 0.1713 | 0.3733 | 0.0601 | 0.4369 | 0.6982 | 0.0890 | 0.7206 | 0.2758 | 0.4942 | 0.7146 | 0.4047 | 0.6371 | 0.0569 | 0.5078 | 0.3551 | 0.6593 | 0.9724 | 0.5445 | 0.3631 | 0.4124 | 0.1904 | 0.7666 | 0.0881 | 0.9053 | 0.6093 | 0.5515 | 0.7196 | 0.2358 | 0.8516 | 0.8760 | 0.6968 | 0.3984 | 0.7784 | 0.8869 | 0.8103 | 0.0678 | 0.7992 | 0.4688 | 0.9772 | 0.1475 | 0.8377 | 0.6754 | 0.7947 | 0.2093 | 0.1357 | 0.3680 | 0.8806 | 0.3840 | 0.3041 | 0.5219 | 0.7025 | 0.2772 | 0.7202 | 0.0972 | 0.666 | 0.4286 | 0.6250 | 0.9593 | 0.4838 | 0.4038 | 0.8337 | 0.5215 | 0.7515 | 0.1794 | 0.7442 | 0.4199 | 0.5193 | 0.7146 | 0.0754 | 0.2063 | 0.6245 | 0.2231 | 0.6068 | 0.4928 | 0.4052 | 0.6223 | 0.5386 | 0.0547 | 0.5592 | 0.8244 | 0.8613 | 0.4118 | 0.2604 | 0.9941 | 0.2965 | 0.7084 | 0.1155 | 0.2920 | 0.1187 | 0.4714 | 0.6888 | 0.6701 | 0.7667 | 0.8939 | 0.5984 | 0.8178 | 0.2564 | 0.8735 | 0.2615 | 0.3401 | 0.5937 | 0.8621 | 0.7918 | 0.3490 | 0.8487 | 0.1116 | 0.657 | 0.6230 | 0.8665 | 0.2460 | 0.7898 | 0.1412 | 0.0587 | 0.6858 | 0.5293 |
Significant_in_GSEA_not_in_dcor <- setdiff(rownames(gsea_results_significant),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(nominal_dcor_pvalues[Significant_in_GSEA_not_in_dcor],gsea_results[Significant_in_GSEA_not_in_dcor,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities %>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| LUI_TARGETS_OF_PAX8_PPARG_FUSION | LUI_THYROID_CANCER_CLUSTER_3 | ANDERSEN_LIVER_CANCER_KRT19_UP | REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_ | POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN | MCBRYAN_PUBERTAL_BREAST_3_4WK_DN | REACTOME_INFLUENZA_LIFE_CYCLE | LANDIS_ERBB2_BREAST_TUMORS_324_UP | KEGG_ALZHEIMERS_DISEASE | REACTOME_METABOLISM_OF_RNA | CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP | REACTOME_RESPIRATORY_ELECTRON_TRANSPORT | FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP | REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY | REACTOME_METABOLISM_OF_MRNA | PECE_MAMMARY_STEM_CELL_UP | KEGG_NUCLEOTIDE_EXCISION_REPAIR | TONG_INTERACT_WITH_PTTG1 | EHLERS_ANEUPLOIDY_UP | YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP | KANNAN_TP53_TARGETS_DN | DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN | MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN | REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX | REACTOME_TRANSLATION | REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES | TAKAO_RESPONSE_TO_UVB_RADIATION_UP | BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN | REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE | HUMMERICH_BENIGN_SKIN_TUMOR_UP | HSIAO_HOUSEKEEPING_GENES | JAZAG_TGFB1_SIGNALING_UP | BAE_BRCA1_TARGETS_UP | KEGG_RIBOSOME | NUTT_GBM_VS_AO_GLIOMA_DN | MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP | KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN | REACTOME_METABOLISM_OF_PROTEINS | BILANGES_SERUM_RESPONSE_TRANSLATION | LANDIS_BREAST_CANCER_PROGRESSION_UP | NAKAYAMA_FGF2_TARGETS | HUNSBERGER_EXERCISE_REGULATED_GENES | LUI_THYROID_CANCER_PAX8_PPARG_DN | WENG_POR_TARGETS_GLOBAL_UP | REACTOME_PEPTIDE_CHAIN_ELONGATION | NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON | IRITANI_MAD1_TARGETS_DN | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17 | LEE_LIVER_CANCER_SURVIVAL_DN | REACTOME_SIGNAL_AMPLIFICATION | WANG_RESPONSE_TO_FORSKOLIN_UP | JIANG_AGING_HYPOTHALAMUS_UP | PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN | HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP | KEGG_BASAL_TRANSCRIPTION_FACTORS | OSMAN_BLADDER_CANCER_DN | YANG_BREAST_CANCER_ESR1_UP | ZHAN_MULTIPLE_MYELOMA_HP_UP | PARK_HSC_MARKERS | REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS | WANG_TUMOR_INVASIVENESS_UP | REACTOME_GLOBAL_GENOMIC_NER_GG_NER | GEORGES_CELL_CYCLE_MIR192_TARGETS | MAINA_VHL_TARGETS_DN | CHEN_PDGF_TARGETS | SCHRAMM_INHBA_TARGETS_DN | FAELT_B_CLL_WITH_VH3_21_DN | BOUDOUKHA_BOUND_BY_IGF2BP2 | NATSUME_RESPONSE_TO_INTERFERON_BETA_DN | REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE | GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN | MURAKAMI_UV_RESPONSE_1HR_UP | PID_PI3K_PLC_TRK_PATHWAY | REACTOME_ADP_SIGNALLING_THROUGH_P2RY1 | WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP | CHANGOLKAR_H2AFY_TARGETS_UP | BIDUS_METASTASIS_DN | BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP | PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN | BORLAK_LIVER_CANCER_EGF_UP | REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 | KIM_MYC_AMPLIFICATION_TARGETS_UP | LINDGREN_BLADDER_CANCER_CLUSTER_1_UP | CHANGOLKAR_H2AFY_TARGETS_DN | HORIUCHI_WTAP_TARGETS_DN | SASAKI_ADULT_T_CELL_LEUKEMIA | GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN | REACTOME_INTEGRATION_OF_ENERGY_METABOLISM | DELASERNA_MYOD_TARGETS_UP | KASLER_HDAC7_TARGETS_2_DN | PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN | SHIN_B_CELL_LYMPHOMA_CLUSTER_8 | DOANE_BREAST_CANCER_ESR1_DN | BIOCARTA_AGR_PATHWAY | REACTOME_RNA_POL_I_PROMOTER_OPENING | REACTOME_HDL_MEDIATED_LIPID_TRANSPORT | FAELT_B_CLL_WITH_VH3_21_UP | KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3 | HASLINGER_B_CLL_WITH_6Q21_DELETION | KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN | KEGG_PPAR_SIGNALING_PATHWAY | REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE | MIKKELSEN_MEF_LCP_WITH_H3K27ME3 | XU_GH1_EXOGENOUS_TARGETS_DN | ABE_VEGFA_TARGETS_2HR | FIGUEROA_AML_METHYLATION_CLUSTER_1_DN | REACTOME_LIPOPROTEIN_METABOLISM | BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN | BIOCARTA_UCALPAIN_PATHWAY | ST_T_CELL_SIGNAL_TRANSDUCTION | DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY | HUMMERICH_MALIGNANT_SKIN_TUMOR_DN | CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP | PID_NCADHERIN_PATHWAY | HUMMERICH_BENIGN_SKIN_TUMOR_DN | REACTOME_PACKAGING_OF_TELOMERE_ENDS | LEI_HOXC8_TARGETS_DN | PID_BARD1_PATHWAY | FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP | BIOCARTA_MAL_PATHWAY | XU_AKT1_TARGETS_6HR | PID_INSULIN_GLUCOSE_PATHWAY | REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS | SA_B_CELL_RECEPTOR_COMPLEXES | SCHEIDEREIT_IKK_INTERACTING_PROTEINS | REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM | ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN | BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP | RIZ_ERYTHROID_DIFFERENTIATION_HEMGN | MEISSNER_BRAIN_HCP_WITH_H3K27ME3 | REACTOME_SEMAPHORIN_INTERACTIONS | KUMAR_AUTOPHAGY_NETWORK | SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN | KENNY_CTNNB1_TARGETS_UP | OXFORD_RALA_OR_RALB_TARGETS_UP | LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP | MIKKELSEN_NPC_HCP_WITH_H3K27ME3 | BIOCARTA_HER2_PATHWAY | FIGUEROA_AML_METHYLATION_CLUSTER_3_DN | KYNG_DNA_DAMAGE_BY_4NQO | MULLIGHAN_NPM1_SIGNATURE_3_DN | PID_IL23_PATHWAY | REACTOME_MEIOTIC_RECOMBINATION | MIKKELSEN_MCV6_HCP_WITH_H3K27ME3 | CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP | QI_HYPOXIA | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.3242 | 0.3169 | 0.6956 | 0.0577 | 0.3964 | 0.2715 | 0.6418 | 0.1277 | 0.0665 | 0.6026 | 0.5402 | 0.0833 | 0.3190 | 0.2233 | 0.6035 | 0.6305 | 0.1524 | 0.6864 | 0.4786 | 0.6865 | 0.6018 | 0.4589 | 0.1582 | 0.6642 | 0.6234 | 0.8495 | 0.1709 | 0.1870 | 0.6512 | 0.2299 | 0.6299 | 0.274 | 0.0948 | 0.6750 | 0.4590 | 0.2537 | 0.5339 | 0.5090 | 0.4730 | 0.8673 | 0.0657 | 0.8722 | 0.3549 | 0.6906 | 0.6585 | 0.4450 | 0.1963 | 0.1226 | 0.5119 | 0.4131 | 0.1975 | 0.7851 | 0.1568 | 0.3937 | 0.2215 | 0.4918 | 0.7278 | 0.5095 | 0.6897 | 0.1328 | 0.4148 | 0.0978 | 0.2645 | 0.1632 | 0.0976 | 0.1489 | 0.0918 | 0.4091 | 0.7153 | 0.1259 | 0.0923 | 0.1369 | 0.8203 | 0.4541 | 0.6576 | 0.2362 | 0.0551 | 0.0797 | 0.4075 | 0.2479 | 0.5201 | 0.4268 | 0.1940 | 0.3909 | 0.929 | 0.1703 | 0.1806 | 0.6394 | 0.2736 | 0.936 | 0.3609 | 0.7809 | 0.676 | 0.6122 | 0.9764 | 0.5319 | 0.0598 | 0.629 | 0.3255 | 0.9589 | 0.9908 | 0.2109 | 0.9279 | 0.9903 | 0.5961 | 0.5957 | 0.4794 | 0.2058 | 0.7918 | 0.9702 | 0.1155 | 0.5746 | 0.8472 | 0.937 | 0.9869 | 0.8236 | 0.9576 | 0.5793 | 0.6348 | 0.9058 | 0.9774 | 0.9449 | 0.2072 | 0.5027 | 0.6089 | 0.9481 | 0.5256 | 0.8768 | 0.5279 | 0.9091 | 0.4482 | 0.1135 | 0.7895 | 0.6251 | 0.0716 | 0.3927 | 0.9084 | 0.2451 | 0.1464 | 0.5465 | 0.0748 | 0.8108 | 0.1961 | 0.4147 | 0.2857 | 0.2419 | 0.5951 |
| GSEA | 0.0020 | 0.0040 | 0.0040 | 0.0177 | 0.0020 | 0.0019 | 0.0158 | 0.0000 | 0.0121 | 0.0198 | 0.0199 | 0.0141 | 0.0061 | 0.0100 | 0.0355 | 0.0326 | 0.0115 | 0.0219 | 0.0161 | 0.0256 | 0.0124 | 0.0166 | 0.0020 | 0.0321 | 0.0325 | 0.0059 | 0.0140 | 0.0082 | 0.0383 | 0.0123 | 0.0238 | 0.000 | 0.0219 | 0.0378 | 0.0339 | 0.0125 | 0.0208 | 0.0374 | 0.0429 | 0.0281 | 0.0337 | 0.0185 | 0.0243 | 0.0161 | 0.0383 | 0.0197 | 0.0178 | 0.0378 | 0.0098 | 0.0168 | 0.0429 | 0.0435 | 0.0329 | 0.0367 | 0.0250 | 0.0400 | 0.0382 | 0.0339 | 0.0333 | 0.0468 | 0.0232 | 0.0408 | 0.0376 | 0.0391 | 0.0380 | 0.0193 | 0.0441 | 0.0376 | 0.0437 | 0.0470 | 0.0041 | 0.0443 | 0.0444 | 0.0406 | 0.0279 | 0.0409 | 0.0207 | 0.0449 | 0.0478 | 0.0361 | 0.0406 | 0.0359 | 0.0231 | 0.0319 | 0.041 | 0.0062 | 0.0125 | 0.0161 | 0.0384 | 0.000 | 0.0038 | 0.0020 | 0.002 | 0.0000 | 0.0019 | 0.0061 | 0.0060 | 0.004 | 0.0000 | 0.0080 | 0.0082 | 0.0020 | 0.0041 | 0.0061 | 0.0061 | 0.0040 | 0.0059 | 0.0348 | 0.0249 | 0.0277 | 0.0138 | 0.0142 | 0.0292 | 0.040 | 0.0193 | 0.0488 | 0.0307 | 0.0277 | 0.0357 | 0.0309 | 0.0408 | 0.0480 | 0.0460 | 0.0248 | 0.0472 | 0.0198 | 0.0202 | 0.0233 | 0.0435 | 0.0442 | 0.0239 | 0.0449 | 0.0253 | 0.0335 | 0.0431 | 0.0337 | 0.0422 | 0.0081 | 0.0498 | 0.0313 | 0.0364 | 0.0385 | 0.0452 | 0.0475 | 0.0167 | 0.0485 | 0.0354 |
# stopCluster(cl)
library(ggfortify)
## Loading required package: ggplot2
for (name in (sort(Significant_in_dcor_not_in_GSEA, decreasing = F))){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw())
# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP"
## [1] "AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN"
## [1] "AMIT_EGF_RESPONSE_40_MCF10A"
## [1] "BASAKI_YBX1_TARGETS_UP"
## [1] "BERNARD_PPAPDC1B_TARGETS_UP"
## [1] "BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN"
## [1] "BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP"
## [1] "BHAT_ESR1_TARGETS_VIA_AKT1_UP"
## [1] "BILD_MYC_ONCOGENIC_SIGNATURE"
## [1] "BIOCARTA_CARDIACEGF_PATHWAY"
## [1] "BIOCARTA_CDC42RAC_PATHWAY"
## [1] "BIOCARTA_EDG1_PATHWAY"
## [1] "BIOCARTA_P53HYPOXIA_PATHWAY"
## [1] "BIOCARTA_PAR1_PATHWAY"
## [1] "BIOCARTA_PTDINS_PATHWAY"
## [1] "BIOCARTA_RACCYCD_PATHWAY"
## [1] "BIOCARTA_RAS_PATHWAY"
## [1] "BOCHKIS_FOXA2_TARGETS"
## [1] "BORCZUK_MALIGNANT_MESOTHELIOMA_UP"
## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN"
## [1] "BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP"
## [1] "BROWNE_HCMV_INFECTION_48HR_UP"
## [1] "BROWNE_HCMV_INFECTION_4HR_DN"
## [1] "BROWNE_HCMV_INFECTION_6HR_DN"
## [1] "BRUECKNER_TARGETS_OF_MIRLET7A3_UP"
## [1] "BURTON_ADIPOGENESIS_6"
## [1] "BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN"
## [1] "BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS"
## [1] "CADWELL_ATG16L1_TARGETS_DN"
## [1] "CAFFAREL_RESPONSE_TO_THC_DN"
## [1] "CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP"
## [1] "CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP"
## [1] "CHEBOTAEV_GR_TARGETS_DN"
## [1] "CHEN_ETV5_TARGETS_TESTIS"
## [1] "COATES_MACROPHAGE_M1_VS_M2_DN"
## [1] "COATES_MACROPHAGE_M1_VS_M2_UP"
## [1] "CUI_GLUCOSE_DEPRIVATION"
## [1] "DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP"
## [1] "DAZARD_RESPONSE_TO_UV_NHEK_DN"
## [1] "DE_YY1_TARGETS_UP"
## [1] "DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN"
## [1] "DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER"
## [1] "ENGELMANN_CANCER_PROGENITORS_DN"
## [1] "ENGELMANN_CANCER_PROGENITORS_UP"
## [1] "ENK_UV_RESPONSE_KERATINOCYTE_DN"
## [1] "FARMER_BREAST_CANCER_APOCRINE_VS_BASAL"
## [1] "FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL"
## [1] "FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS"
## [1] "FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN"
## [1] "FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP"
## [1] "FORTSCHEGGER_PHF8_TARGETS_UP"
## [1] "FOSTER_TOLERANT_MACROPHAGE_UP"
## [1] "FRIDMAN_IMMORTALIZATION_DN"
## [1] "FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP"
## [1] "GAJATE_RESPONSE_TO_TRABECTEDIN_UP"
## [1] "GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN"
## [1] "GARY_CD5_TARGETS_DN"
## [1] "GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP"
## [1] "GEISS_RESPONSE_TO_DSRNA_DN"
## [1] "GENTILE_UV_LOW_DOSE_UP"
## [1] "GEORGES_TARGETS_OF_MIR192_AND_MIR215"
## [1] "GOLUB_ALL_VS_AML_DN"
## [1] "GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP"
## [1] "GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN"
## [1] "GUILLAUMOND_KLF10_TARGETS_DN"
## [1] "GUTIERREZ_MULTIPLE_MYELOMA_UP"
## [1] "HASLINGER_B_CLL_WITH_MUTATED_VH_GENES"
## [1] "HEIDENBLAD_AMPLICON_12P11_12_UP"
## [1] "HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS"
## [1] "HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN"
## [1] "HORTON_SREBF_TARGETS"
## [1] "HOUSTIS_ROS"
## [1] "HU_ANGIOGENESIS_DN"
## [1] "ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN"
## [1] "IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP"
## [1] "JAEGER_METASTASIS_DN"
## [1] "JOHNSTONE_PARVB_TARGETS_3_UP"
## [1] "JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP"
## [1] "KASLER_HDAC7_TARGETS_1_DN"
## [1] "KEEN_RESPONSE_TO_ROSIGLITAZONE_UP"
## [1] "KEGG_COLORECTAL_CANCER"
## [1] "KEGG_PYRIMIDINE_METABOLISM"
## [1] "KEGG_RNA_POLYMERASE"
## [1] "KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"
## [1] "KEGG_STEROID_BIOSYNTHESIS"
## [1] "KENNY_CTNNB1_TARGETS_DN"
## [1] "KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP"
## [1] "LABBE_WNT3A_TARGETS_DN"
## [1] "LAMB_CCND1_TARGETS"
## [1] "LEE_DIFFERENTIATING_T_LYMPHOCYTE"
## [1] "LEE_TARGETS_OF_PTCH1_AND_SUFU_DN"
## [1] "LEIN_CHOROID_PLEXUS_MARKERS"
## [1] "LENAOUR_DENDRITIC_CELL_MATURATION_DN"
## [1] "LI_INDUCED_T_TO_NATURAL_KILLER_DN"
## [1] "LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP"
## [1] "LIN_NPAS4_TARGETS_UP"
## [1] "LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q"
## [1] "LIU_PROSTATE_CANCER_UP"
## [1] "LIU_SOX4_TARGETS_UP"
## [1] "MA_MYELOID_DIFFERENTIATION_DN"
## [1] "MACLACHLAN_BRCA1_TARGETS_UP"
## [1] "MANALO_HYPOXIA_DN"
## [1] "MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5"
## [1] "MARKS_HDAC_TARGETS_UP"
## [1] "MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP"
## [1] "MASSARWEH_RESPONSE_TO_ESTRADIOL"
## [1] "MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN"
## [1] "MCCLUNG_COCAINE_REWARD_5D"
## [1] "MENSE_HYPOXIA_UP"
## [1] "MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED"
## [1] "MIKKELSEN_ES_ICP_WITH_H3K4ME3"
## [1] "MISSIAGLIA_REGULATED_BY_METHYLATION_UP"
## [1] "MITSIADES_RESPONSE_TO_APLIDIN_UP"
## [1] "MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN"
## [1] "MOREIRA_RESPONSE_TO_TSA_UP"
## [1] "MORI_SMALL_PRE_BII_LYMPHOCYTE_UP"
## [1] "MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP"
## [1] "MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP"
## [1] "MULLIGHAN_NPM1_SIGNATURE_3_UP"
## [1] "MURAKAMI_UV_RESPONSE_24HR"
## [1] "MURAKAMI_UV_RESPONSE_6HR_DN"
## [1] "NADLER_HYPERGLYCEMIA_AT_OBESITY"
## [1] "NAGASHIMA_NRG1_SIGNALING_DN"
## [1] "NOJIMA_SFRP2_TARGETS_UP"
## [1] "NUYTTEN_NIPP1_TARGETS_UP"
## [1] "ODONNELL_METASTASIS_DN"
## [1] "ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP"
## [1] "OISHI_CHOLANGIOMA_STEM_CELL_LIKE_DN"
## [1] "ONDER_CDH1_TARGETS_1_UP"
## [1] "OUILLETTE_CLL_13Q14_DELETION_DN"
## [1] "PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7"
## [1] "PENG_RAPAMYCIN_RESPONSE_UP"
## [1] "PETRETTO_CARDIAC_HYPERTROPHY"
## [1] "PETRETTO_HEART_MASS_QTL_CIS_DN"
## [1] "PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP"
## [1] "PETROVA_PROX1_TARGETS_UP"
## [1] "PID_AVB3_INTEGRIN_PATHWAY"
## [1] "PID_AVB3_OPN_PATHWAY"
## [1] "PID_ECADHERIN_KERATINOCYTE_PATHWAY"
## [1] "PID_ECADHERIN_NASCENT_AJ_PATHWAY"
## [1] "PID_EPHA_FWDPATHWAY"
## [1] "PID_EPHA2_FWD_PATHWAY"
## [1] "PID_IL4_2PATHWAY"
## [1] "PID_LIS1_PATHWAY"
## [1] "PID_P53_REGULATION_PATHWAY"
## [1] "PID_PRL_SIGNALING_EVENTS_PATHWAY"
## [1] "PID_PTP1B_PATHWAY"
## [1] "PID_S1P_S1P1_PATHWAY"
## [1] "PID_S1P_S1P2_PATHWAY"
## [1] "PID_S1P_S1P3_PATHWAY"
## [1] "PID_SYNDECAN_4_PATHWAY"
## [1] "PID_TGFBR_PATHWAY"
## [1] "PID_VEGFR1_2_PATHWAY"
## [1] "PID_WNT_NONCANONICAL_PATHWAY"
## [1] "PLASARI_NFIC_TARGETS_BASAL_UP"
## [1] "PLASARI_TGFB1_TARGETS_10HR_DN"
## [1] "PUJANA_BRCA2_PCC_NETWORK"
## [1] "QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2"
## [1] "RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP"
## [1] "RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN"
## [1] "REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT"
## [1] "REACTOME_CHOLESTEROL_BIOSYNTHESIS"
## [1] "REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX"
## [1] "REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX"
## [1] "REACTOME_G_ALPHA1213_SIGNALLING_EVENTS"
## [1] "REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA"
## [1] "REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING"
## [1] "REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE"
## [1] "REACTOME_MICRORNA_MIRNA_BIOGENESIS"
## [1] "REACTOME_MRNA_SPLICING_MINOR_PATHWAY"
## [1] "REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING"
## [1] "REACTOME_PEROXISOMAL_LIPID_METABOLISM"
## [1] "REACTOME_PI3K_AKT_ACTIVATION"
## [1] "REACTOME_REGULATORY_RNA_PATHWAYS"
## [1] "REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING"
## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION"
## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER"
## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER"
## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION"
## [1] "REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING"
## [1] "REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE"
## [1] "REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT"
## [1] "RICKMAN_METASTASIS_UP"
## [1] "RIGGI_EWING_SARCOMA_PROGENITOR_DN"
## [1] "RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP"
## [1] "RODWELL_AGING_KIDNEY_NO_BLOOD_DN"
## [1] "ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP"
## [1] "SA_TRKA_RECEPTOR"
## [1] "SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN"
## [1] "SANSOM_APC_TARGETS_DN"
## [1] "SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1"
## [1] "SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP"
## [1] "SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP"
## [1] "SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP"
## [1] "SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY"
## [1] "SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP"
## [1] "SHEN_SMARCA2_TARGETS_UP"
## [1] "SHEPARD_CRUSH_AND_BURN_MUTANT_UP"
## [1] "SHI_SPARC_TARGETS_UP"
## [1] "SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN"
## [1] "SMITH_TERT_TARGETS_DN"
## [1] "TARTE_PLASMA_CELL_VS_PLASMABLAST_DN"
## [1] "TIAN_TNF_SIGNALING_NOT_VIA_NFKB"
## [1] "TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP"
## [1] "UEDA_PERIFERAL_CLOCK"
## [1] "VANTVEER_BREAST_CANCER_ESR1_UP"
## [1] "VARELA_ZMPSTE24_TARGETS_UP"
## [1] "VERHAAK_GLIOBLASTOMA_NEURAL"
## [1] "VERRECCHIA_EARLY_RESPONSE_TO_TGFB1"
## [1] "WALLACE_PROSTATE_CANCER_RACE_UP"
## [1] "WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN"
## [1] "WANG_SMARCE1_TARGETS_UP"
## [1] "WANG_TARGETS_OF_MLL_CBP_FUSION_DN"
## [1] "WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP"
## [1] "WHITFIELD_CELL_CYCLE_G2"
## [1] "WIERENGA_STAT5A_TARGETS_GROUP1"
## [1] "WIERENGA_STAT5A_TARGETS_GROUP2"
## [1] "WIERENGA_STAT5A_TARGETS_UP"
## [1] "WINNEPENNINCKX_MELANOMA_METASTASIS_DN"
## [1] "WINZEN_DEGRADED_VIA_KHSRP"
## [1] "YAGI_AML_RELAPSE_PROGNOSIS"
## [1] "YAGI_AML_WITH_T_8_21_TRANSLOCATION"
## [1] "YAMASHITA_METHYLATED_IN_PROSTATE_CANCER"
## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1"
## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5"
## [1] "ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN"
## [1] "ZHANG_TLX_TARGETS_60HR_DN"
## [1] "ZHENG_FOXP3_TARGETS_IN_THYMUS_UP"
rownames(gsea_results_significant)
## [1] "LUI_TARGETS_OF_PAX8_PPARG_FUSION"
## [2] "MOOTHA_VOXPHOS"
## [3] "LUI_THYROID_CANCER_CLUSTER_3"
## [4] "ANDERSEN_LIVER_CANCER_KRT19_UP"
## [5] "REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_"
## [6] "POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN"
## [7] "MCBRYAN_PUBERTAL_BREAST_3_4WK_DN"
## [8] "REACTOME_INFLUENZA_LIFE_CYCLE"
## [9] "LANDIS_ERBB2_BREAST_TUMORS_324_UP"
## [10] "KEGG_ALZHEIMERS_DISEASE"
## [11] "REACTOME_METABOLISM_OF_RNA"
## [12] "CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP"
## [13] "REACTOME_RESPIRATORY_ELECTRON_TRANSPORT"
## [14] "FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP"
## [15] "FERRANDO_TAL1_NEIGHBORS"
## [16] "REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY"
## [17] "REACTOME_METABOLISM_OF_MRNA"
## [18] "PECE_MAMMARY_STEM_CELL_UP"
## [19] "KEGG_NUCLEOTIDE_EXCISION_REPAIR"
## [20] "LANDIS_ERBB2_BREAST_TUMORS_65_UP"
## [21] "KEGG_OXIDATIVE_PHOSPHORYLATION"
## [22] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13"
## [23] "TONG_INTERACT_WITH_PTTG1"
## [24] "EHLERS_ANEUPLOIDY_UP"
## [25] "YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP"
## [26] "KANNAN_TP53_TARGETS_DN"
## [27] "DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN"
## [28] "MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN"
## [29] "REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX"
## [30] "REACTOME_TRANSLATION"
## [31] "REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES"
## [32] "TAKAO_RESPONSE_TO_UVB_RADIATION_UP"
## [33] "BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN"
## [34] "KEGG_HUNTINGTONS_DISEASE"
## [35] "REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE"
## [36] "HUMMERICH_BENIGN_SKIN_TUMOR_UP"
## [37] "HSIAO_HOUSEKEEPING_GENES"
## [38] "JAZAG_TGFB1_SIGNALING_UP"
## [39] "BAE_BRCA1_TARGETS_UP"
## [40] "KEGG_RIBOSOME"
## [41] "NUTT_GBM_VS_AO_GLIOMA_DN"
## [42] "MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP"
## [43] "KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN"
## [44] "REACTOME_METABOLISM_OF_PROTEINS"
## [45] "BILANGES_SERUM_RESPONSE_TRANSLATION"
## [46] "REACTOME_NUCLEOTIDE_EXCISION_REPAIR"
## [47] "LANDIS_BREAST_CANCER_PROGRESSION_UP"
## [48] "WONG_MITOCHONDRIA_GENE_MODULE"
## [49] "NAKAYAMA_FGF2_TARGETS"
## [50] "HUNSBERGER_EXERCISE_REGULATED_GENES"
## [51] "REACTOME_TRANSCRIPTION_COUPLED_NER_TC_NER"
## [52] "LUI_THYROID_CANCER_PAX8_PPARG_DN"
## [53] "WENG_POR_TARGETS_GLOBAL_UP"
## [54] "FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN"
## [55] "MORI_IMMATURE_B_LYMPHOCYTE_UP"
## [56] "REACTOME_PEPTIDE_CHAIN_ELONGATION"
## [57] "NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON"
## [58] "IRITANI_MAD1_TARGETS_DN"
## [59] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17"
## [60] "LEE_LIVER_CANCER_SURVIVAL_DN"
## [61] "REACTOME_SIGNAL_AMPLIFICATION"
## [62] "LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_UP"
## [63] "WANG_RESPONSE_TO_FORSKOLIN_UP"
## [64] "JIANG_AGING_HYPOTHALAMUS_UP"
## [65] "PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN"
## [66] "HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP"
## [67] "KEGG_BASAL_TRANSCRIPTION_FACTORS"
## [68] "OSMAN_BLADDER_CANCER_DN"
## [69] "YANG_BREAST_CANCER_ESR1_UP"
## [70] "ZHAN_MULTIPLE_MYELOMA_HP_UP"
## [71] "PARK_HSC_MARKERS"
## [72] "REACTOME_MRNA_CAPPING"
## [73] "GROSS_HYPOXIA_VIA_HIF1A_UP"
## [74] "REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS"
## [75] "WANG_TUMOR_INVASIVENESS_UP"
## [76] "REACTOME_GLOBAL_GENOMIC_NER_GG_NER"
## [77] "GEORGES_CELL_CYCLE_MIR192_TARGETS"
## [78] "MAINA_VHL_TARGETS_DN"
## [79] "CHEN_PDGF_TARGETS"
## [80] "SCHRAMM_INHBA_TARGETS_DN"
## [81] "FAELT_B_CLL_WITH_VH3_21_DN"
## [82] "BOUDOUKHA_BOUND_BY_IGF2BP2"
## [83] "NATSUME_RESPONSE_TO_INTERFERON_BETA_DN"
## [84] "REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE"
## [85] "GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN"
## [86] "MURAKAMI_UV_RESPONSE_1HR_UP"
## [87] "PID_PI3K_PLC_TRK_PATHWAY"
## [88] "REACTOME_ADP_SIGNALLING_THROUGH_P2RY1"
## [89] "WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP"
## [90] "CHANGOLKAR_H2AFY_TARGETS_UP"
## [91] "BIDUS_METASTASIS_DN"
## [92] "BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP"
## [93] "PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN"
## [94] "BORLAK_LIVER_CANCER_EGF_UP"
## [95] "REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS"
## [96] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9"
## [97] "KIM_MYC_AMPLIFICATION_TARGETS_UP"
## [98] "LINDGREN_BLADDER_CANCER_CLUSTER_1_UP"
## [99] "CHANGOLKAR_H2AFY_TARGETS_DN"
## [100] "HORIUCHI_WTAP_TARGETS_DN"
## [101] "SASAKI_ADULT_T_CELL_LEUKEMIA"
## [102] "GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN"
## [103] "REACTOME_DNA_REPAIR"
## [104] "REACTOME_INTEGRATION_OF_ENERGY_METABOLISM"
## [105] "PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP"
## [106] "DELASERNA_MYOD_TARGETS_UP"
## [107] "KASLER_HDAC7_TARGETS_2_DN"
## [108] "PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN"
## [109] "SHIN_B_CELL_LYMPHOMA_CLUSTER_8"
## [110] "DOANE_BREAST_CANCER_ESR1_DN"
## [111] "BIOCARTA_AGR_PATHWAY"
## [112] "REACTOME_RNA_POL_I_PROMOTER_OPENING"
## [113] "REACTOME_HDL_MEDIATED_LIPID_TRANSPORT"
## [114] "REACTOME_MEIOTIC_SYNAPSIS"
## [115] "FAELT_B_CLL_WITH_VH3_21_UP"
## [116] "KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3"
## [117] "HASLINGER_B_CLL_WITH_6Q21_DELETION"
## [118] "KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN"
## [119] "KEGG_PPAR_SIGNALING_PATHWAY"
## [120] "REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE"
## [121] "MIKKELSEN_MEF_LCP_WITH_H3K27ME3"
## [122] "XU_GH1_EXOGENOUS_TARGETS_DN"
## [123] "ABE_VEGFA_TARGETS_2HR"
## [124] "FIGUEROA_AML_METHYLATION_CLUSTER_1_DN"
## [125] "REACTOME_LIPOPROTEIN_METABOLISM"
## [126] "BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN"
## [127] "BIOCARTA_UCALPAIN_PATHWAY"
## [128] "ST_T_CELL_SIGNAL_TRANSDUCTION"
## [129] "DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY"
## [130] "OHGUCHI_LIVER_HNF4A_TARGETS_UP"
## [131] "HUMMERICH_MALIGNANT_SKIN_TUMOR_DN"
## [132] "CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP"
## [133] "PID_NCADHERIN_PATHWAY"
## [134] "HUMMERICH_BENIGN_SKIN_TUMOR_DN"
## [135] "REACTOME_PACKAGING_OF_TELOMERE_ENDS"
## [136] "LEI_HOXC8_TARGETS_DN"
## [137] "REACTOME_MEIOSIS"
## [138] "PID_BARD1_PATHWAY"
## [139] "FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP"
## [140] "BIOCARTA_MAL_PATHWAY"
## [141] "XU_AKT1_TARGETS_6HR"
## [142] "PID_INSULIN_GLUCOSE_PATHWAY"
## [143] "REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS"
## [144] "SA_B_CELL_RECEPTOR_COMPLEXES"
## [145] "SCHEIDEREIT_IKK_INTERACTING_PROTEINS"
## [146] "SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER"
## [147] "REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM"
## [148] "ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN"
## [149] "GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_UP"
## [150] "BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP"
## [151] "RIZ_ERYTHROID_DIFFERENTIATION_HEMGN"
## [152] "MEISSNER_BRAIN_HCP_WITH_H3K27ME3"
## [153] "REACTOME_SEMAPHORIN_INTERACTIONS"
## [154] "KUMAR_AUTOPHAGY_NETWORK"
## [155] "SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN"
## [156] "KENNY_CTNNB1_TARGETS_UP"
## [157] "OXFORD_RALA_OR_RALB_TARGETS_UP"
## [158] "LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP"
## [159] "MIKKELSEN_NPC_HCP_WITH_H3K27ME3"
## [160] "BIOCARTA_HER2_PATHWAY"
## [161] "FIGUEROA_AML_METHYLATION_CLUSTER_3_DN"
## [162] "KYNG_DNA_DAMAGE_BY_4NQO"
## [163] "MULLIGHAN_NPM1_SIGNATURE_3_DN"
## [164] "PID_IL23_PATHWAY"
## [165] "REACTOME_MEIOTIC_RECOMBINATION"
## [166] "MIKKELSEN_MCV6_HCP_WITH_H3K27ME3"
## [167] "REACTOME_CHROMOSOME_MAINTENANCE"
## [168] "CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP"
## [169] "QI_HYPOXIA"
## [170] "SMID_BREAST_CANCER_ERBB2_UP"
for (name in (Significant_in_GSEA_not_in_dcor)){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name"))
# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "LUI_TARGETS_OF_PAX8_PPARG_FUSION"
## [1] "LUI_THYROID_CANCER_CLUSTER_3"
## [1] "ANDERSEN_LIVER_CANCER_KRT19_UP"
## [1] "REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_"
## [1] "POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN"
## [1] "MCBRYAN_PUBERTAL_BREAST_3_4WK_DN"
## [1] "REACTOME_INFLUENZA_LIFE_CYCLE"
## [1] "LANDIS_ERBB2_BREAST_TUMORS_324_UP"
## [1] "KEGG_ALZHEIMERS_DISEASE"
## [1] "REACTOME_METABOLISM_OF_RNA"
## [1] "CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP"
## [1] "REACTOME_RESPIRATORY_ELECTRON_TRANSPORT"
## [1] "FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP"
## [1] "REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY"
## [1] "REACTOME_METABOLISM_OF_MRNA"
## [1] "PECE_MAMMARY_STEM_CELL_UP"
## [1] "KEGG_NUCLEOTIDE_EXCISION_REPAIR"
## [1] "TONG_INTERACT_WITH_PTTG1"
## [1] "EHLERS_ANEUPLOIDY_UP"
## [1] "YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP"
## [1] "KANNAN_TP53_TARGETS_DN"
## [1] "DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN"
## [1] "MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN"
## [1] "REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX"
## [1] "REACTOME_TRANSLATION"
## [1] "REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES"
## [1] "TAKAO_RESPONSE_TO_UVB_RADIATION_UP"
## [1] "BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN"
## [1] "REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE"
## [1] "HUMMERICH_BENIGN_SKIN_TUMOR_UP"
## [1] "HSIAO_HOUSEKEEPING_GENES"
## [1] "JAZAG_TGFB1_SIGNALING_UP"
## [1] "BAE_BRCA1_TARGETS_UP"
## [1] "KEGG_RIBOSOME"
## [1] "NUTT_GBM_VS_AO_GLIOMA_DN"
## [1] "MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP"
## [1] "KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN"
## [1] "REACTOME_METABOLISM_OF_PROTEINS"
## [1] "BILANGES_SERUM_RESPONSE_TRANSLATION"
## [1] "LANDIS_BREAST_CANCER_PROGRESSION_UP"
## [1] "NAKAYAMA_FGF2_TARGETS"
## [1] "HUNSBERGER_EXERCISE_REGULATED_GENES"
## [1] "LUI_THYROID_CANCER_PAX8_PPARG_DN"
## [1] "WENG_POR_TARGETS_GLOBAL_UP"
## [1] "REACTOME_PEPTIDE_CHAIN_ELONGATION"
## [1] "NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON"
## [1] "IRITANI_MAD1_TARGETS_DN"
## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17"
## [1] "LEE_LIVER_CANCER_SURVIVAL_DN"
## [1] "REACTOME_SIGNAL_AMPLIFICATION"
## [1] "WANG_RESPONSE_TO_FORSKOLIN_UP"
## [1] "JIANG_AGING_HYPOTHALAMUS_UP"
## [1] "PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN"
## [1] "HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP"
## [1] "KEGG_BASAL_TRANSCRIPTION_FACTORS"
## [1] "OSMAN_BLADDER_CANCER_DN"
## [1] "YANG_BREAST_CANCER_ESR1_UP"
## [1] "ZHAN_MULTIPLE_MYELOMA_HP_UP"
## [1] "PARK_HSC_MARKERS"
## [1] "REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS"
## [1] "WANG_TUMOR_INVASIVENESS_UP"
## [1] "REACTOME_GLOBAL_GENOMIC_NER_GG_NER"
## [1] "GEORGES_CELL_CYCLE_MIR192_TARGETS"
## [1] "MAINA_VHL_TARGETS_DN"
## [1] "CHEN_PDGF_TARGETS"
## [1] "SCHRAMM_INHBA_TARGETS_DN"
## [1] "FAELT_B_CLL_WITH_VH3_21_DN"
## [1] "BOUDOUKHA_BOUND_BY_IGF2BP2"
## [1] "NATSUME_RESPONSE_TO_INTERFERON_BETA_DN"
## [1] "REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE"
## [1] "GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN"
## [1] "MURAKAMI_UV_RESPONSE_1HR_UP"
## [1] "PID_PI3K_PLC_TRK_PATHWAY"
## [1] "REACTOME_ADP_SIGNALLING_THROUGH_P2RY1"
## [1] "WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP"
## [1] "CHANGOLKAR_H2AFY_TARGETS_UP"
## [1] "BIDUS_METASTASIS_DN"
## [1] "BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP"
## [1] "PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN"
## [1] "BORLAK_LIVER_CANCER_EGF_UP"
## [1] "REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS"
## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9"
## [1] "KIM_MYC_AMPLIFICATION_TARGETS_UP"
## [1] "LINDGREN_BLADDER_CANCER_CLUSTER_1_UP"
## [1] "CHANGOLKAR_H2AFY_TARGETS_DN"
## [1] "HORIUCHI_WTAP_TARGETS_DN"
## [1] "SASAKI_ADULT_T_CELL_LEUKEMIA"
## [1] "GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN"
## [1] "REACTOME_INTEGRATION_OF_ENERGY_METABOLISM"
## [1] "DELASERNA_MYOD_TARGETS_UP"
## [1] "KASLER_HDAC7_TARGETS_2_DN"
## [1] "PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN"
## [1] "SHIN_B_CELL_LYMPHOMA_CLUSTER_8"
## [1] "DOANE_BREAST_CANCER_ESR1_DN"
## [1] "BIOCARTA_AGR_PATHWAY"
## [1] "REACTOME_RNA_POL_I_PROMOTER_OPENING"
## [1] "REACTOME_HDL_MEDIATED_LIPID_TRANSPORT"
## [1] "FAELT_B_CLL_WITH_VH3_21_UP"
## [1] "KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3"
## [1] "HASLINGER_B_CLL_WITH_6Q21_DELETION"
## [1] "KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN"
## [1] "KEGG_PPAR_SIGNALING_PATHWAY"
## [1] "REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE"
## [1] "MIKKELSEN_MEF_LCP_WITH_H3K27ME3"
## [1] "XU_GH1_EXOGENOUS_TARGETS_DN"
## [1] "ABE_VEGFA_TARGETS_2HR"
## [1] "FIGUEROA_AML_METHYLATION_CLUSTER_1_DN"
## [1] "REACTOME_LIPOPROTEIN_METABOLISM"
## [1] "BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN"
## [1] "BIOCARTA_UCALPAIN_PATHWAY"
## [1] "ST_T_CELL_SIGNAL_TRANSDUCTION"
## [1] "DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY"
## [1] "HUMMERICH_MALIGNANT_SKIN_TUMOR_DN"
## [1] "CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP"
## [1] "PID_NCADHERIN_PATHWAY"
## [1] "HUMMERICH_BENIGN_SKIN_TUMOR_DN"
## [1] "REACTOME_PACKAGING_OF_TELOMERE_ENDS"
## [1] "LEI_HOXC8_TARGETS_DN"
## [1] "PID_BARD1_PATHWAY"
## [1] "FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP"
## [1] "BIOCARTA_MAL_PATHWAY"
## [1] "XU_AKT1_TARGETS_6HR"
## [1] "PID_INSULIN_GLUCOSE_PATHWAY"
## [1] "REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS"
## [1] "SA_B_CELL_RECEPTOR_COMPLEXES"
## [1] "SCHEIDEREIT_IKK_INTERACTING_PROTEINS"
## [1] "REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM"
## [1] "ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN"
## [1] "BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP"
## [1] "RIZ_ERYTHROID_DIFFERENTIATION_HEMGN"
## [1] "MEISSNER_BRAIN_HCP_WITH_H3K27ME3"
## [1] "REACTOME_SEMAPHORIN_INTERACTIONS"
## [1] "KUMAR_AUTOPHAGY_NETWORK"
## [1] "SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN"
## [1] "KENNY_CTNNB1_TARGETS_UP"
## [1] "OXFORD_RALA_OR_RALB_TARGETS_UP"
## [1] "LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP"
## [1] "MIKKELSEN_NPC_HCP_WITH_H3K27ME3"
## [1] "BIOCARTA_HER2_PATHWAY"
## [1] "FIGUEROA_AML_METHYLATION_CLUSTER_3_DN"
## [1] "KYNG_DNA_DAMAGE_BY_4NQO"
## [1] "MULLIGHAN_NPM1_SIGNATURE_3_DN"
## [1] "PID_IL23_PATHWAY"
## [1] "REACTOME_MEIOTIC_RECOMBINATION"
## [1] "MIKKELSEN_MCV6_HCP_WITH_H3K27ME3"
## [1] "CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP"
## [1] "QI_HYPOXIA"